Better way for stopping simulations on timeline?
If you keep the mouse over the pause button in the timeline until the next frame is updated, it should register your click eventually. AFAIK the problem is that during a frame update, all of Blender's UI is locked (including all hotkeys), so consequently, nothing will be able to stop it while updating an individual frame. 

This is universal for anything in Blender (and I think any app) that locks up the interface for a while. It doesn't log the position of the mouse until it has time to handle the click event. Sort of unfortunate, but that's just the way it works.